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Model & other Organisms for biopharmaceutical
research Glossary & taxonomy
Evolving terminology for emerging
technologies
Suggestions? Comments? Questions? Mary Chitty MSLS mchitty@healthtech.com
Last revised
January 09, 2020
Biology & chemistry
term index
Related glossaries include Functional
genomics,
Nomenclature.
amoeba: See Dictyostelium discoideum
animal model: A laboratory animal useful for medical research
because it has specific characteristics that resemble a human disease or
disorder. Scientists can create animal models, usually laboratory mice,
by transferring new genes into them. [NHGRI]
Experts in the
pharmaceutical industry, as well as some at the U.S. Food and Drug
Administration (FDA), have identified inadequate animal models as being one of
the major hurdles in drug discovery and development. Pharmaceutical companies
have long used model organisms, both in preclinical studies as well as for
toxicity testing. Now, beyond simply testing drugs in animals to ascertain their
safety, researchers are increasingly seeking animal models not only of specific
diseases, but also of the particular pathways being targeted. CHA
Cambridge Healthtech Advisors, Model
Animal Systems: Emerging Applications and Commercial Opportunities in Drug
Discovery and Development, report 2004 Contrast with model organisms.
Arabidopsis thaliana:
The first plant genome to be completely sequenced.
Not of agricultural significance, but a model system for plant development,
genetics and physiology. [Nature 408 (6814): 816- 26, 14 Dec. 2000
Arabidopsis (brassica or mustard family) - The Arabidopsis Information
Resource (TAIR) http://www.arabidopsis.org/
Caenorhabditis elegans (C.
elegans) : Nematode worm, a model organism, the first multicellular
organism to have a completely sequenced genome (97 megabases of DNA with
19,099 predicted protein-coding genes) as of December 11 1998. C.
elegans Sequencing Consortium "Genome Sequence of the Nematode
C.
Elegans" Science 282:2012 Dec 11, 1998
WormBase
http://www.wormbase.org/
congenic mice:
Mouse strains constructed to possess identical
genotypes except for a difference at a single gene locus. MeSH, 1999
Dictyostelium discoideum
(amoeba):
A genus of protozoa, formerly also considered a fungus. Its natural habitat
is decaying forest leaves, where it feeds on bacteria. D. discoideum is
the best- known species and is widely used in biomedical research. MeSH, 1979 Dictybase, Northwestern Univ. US http://dictybase.org/
Part of the Virtual Library
disease models:
Genetically
modified mice have proven effective in the identification of new gene function
and of novel drug targets and appropriate disease models are powerful tools for
validation of such targets while facilitating disease and patient stratification
studies at the same time. There is an marked increase in the use of mouse and
other models for translational research purposes and a drive toward expediting
the in vivo evaluation of in vitro selected molecules by
developing animal models more predictive of therapeutic efficacy.
Drosophila:
A genus of small, two- winged flies containing
approximately 900 described species. These organisms are the most extensively
studied of all genera from the standpoint of genetics and cytology.
[MeSH Drosophila melanogaster:
A species of fruit fly much used in genetics because of the large size
of its chromosomes. MeSH, 1972
Despite the fact that Drosophila
is a much studied organism, Celera (working with BDGP Berkeley Drosophila
Genome Project annotators) identified thousands of new genes in
commercially important protein families such as kinases, ion channels,
secreted proteins, and G-protein coupled receptors during the sequencing
phase.
Drosophila Genome
Special
section in Science 287: 2181- 2225, 2272- 2274, March 24, 2000.
Berkeley Drosophila Genome
Project BDGP, Univ. of California-Berkeley, US http://www.fruitfly.org/
Curated annotated informatics database
from the Berkeley and European Drosophila genome projects, with
annotations from the literature, comparative sequence analysis and the
FlyBase research community.
Flybase
A Database of Drosophila Genes & Genomes
http://flybase.org/
Interactive Fly, Society of Developmental
Biology
http://www.sdbonline.org/sites/fly/aimain/1aahome.htm
WWW Virtual Library: Drosophila http://ceolas.org/fly/
Drosophila proteins:
Proteins that originate from insect species
belonging to the genus DROSOPHILA. The proteins from the most intensely studied
species of Drosophila, DROSOPHILA MELANOGASTER, are the subject of much interest
in the area of MORPHOGENESIS and development. MeSH, 2002
E. coli Escherichia coli:
Common bacterium
that has been studied intensively by geneticists because of its small genome
size, normal lack of pathogenicity, and ease of growth in the laboratory. [DOE]
The archetypal model organism...has
revealed many fundamental principles of cell metabolism, macromolecular
synthesis, and gene regulation. It is better characterized than any other
cell. But there remains so much more to learn. [Kenneth Rudd 'New tools
for an old workhorse" Nature Biotechnology 18: 1241-1242 Dec. 2000]
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria
(GRAM- NEGATIVE FACULTATIVELY ANEROBIC RODS) commonly found in the lower part of
the intestine of warm- blooded animals. It is usually nonpathogenic, but some
strains are known to produce DIARRHEA and pyogenic infections. MeSH
The preeminent French scientist and 1965 Nobel laureate Jacques Monod famously remarked, "What's true for E. coli is true for an elephant."
https://www.cshl.edu/new-book-distills-essence-of-gene-regulation-and-more/
E. coli genome
Nature 409 (6819), 529-533 Jan. 25, 2001.
Profiling of Escherichia coli chromosome
(PEC),
Shared Information
of GENetic Resource, National Institute of Genetics, Japan http://www.shigen.nig.ac.jp/ecoli/pec/index.jsp
Database has been constructed to compile any relevant information that could help to characterize the
E. coli genome, especially with respect to discovering the function of each gene.
fly, fruit
fly: See Drosophila.
frog: See Xenopus.
GMO Genetically Modified Organism:
Organisms whose GENOME has been
changed by a GENETIC ENGINEERING technique. MeSH, 2002
Often
restricted to modification by biotechnology related techniques (though various
forms of non- molecular agricultural and veterinary modifications have been
practiced for centuries (plant hybridization, breeding of race horses, etc.). Related term
transgenic
Gene OntologyTM Consortium: Functional
genomics glossary
knockout mice:
Mice whose genome contains a gene whose function has
been disrupted, or "knocked- out". A common method of producing
disabled genes using recombinant DNA technology is by inserting an antibiotic
resistance gene into the normal DNA sequence of a clone of the gene being
studied. This disrupts the gene's action, thereby preventing it from making an
active protein product. Cells in which this transfer is successful are then
injected into mouse embryos, producing chimeric mice. These mice are bred to
yield a strain in which all the cells contain the knocked- out gene. Knockout
mice are used as animal models for various diseases, such as cystic fibrosis,
and are helping to clarify the functions of the genes studied within the fields
of immunology, cancer genetics, and developmental
biology. Mesh, 1994
Knockout-mouse
technology is considered an essential and standard technique in functional
genomics and target validation.
knockout
rats: Wikipedia http://en.wikipedia.org/wiki/Knockout_rat
mice: See congenic mice, knockout mice, mouse
model organisms: Organisms used as models for studying the
biological processes underlying states of health and disease, as well as the
effects of particular compounds. Among the model organisms most commonly studied
are mice, yeast, worms, fruit flies, and zebrafish. Because they
are amenable to linking genes with cellular
and physiological responses, simple model organisms are expected to be highly
useful in understanding evolution and development with a biomedical perspective.
Model
organisms are of key importance in both creating databases of gene sequences for
homology searching, and as platforms for investigating the biology of
genes of interest. Over the last few years, the use - and sophistication - of
such models has increased substantially. Findings from the recent publications
by the Human Genome Project and Celera Genomics support that homology
between human and animal- model genes and proteins is significant, particularly
among vertebrate species. Still, the conservation of genes and genetic pathways
between humans and invertebrate organisms is great enough that some of these
organisms have become critical model systems.
Cell Biology: Whither
Model Organism Research?, Stanley Fields and Mark Johnston, Science
307 (5717): 1885-1886, 25 March 2005
HOMOLOGENE,
NCBI, US http://www.ncbi.nlm.nih.gov/HomoloGene/ A homology resource which includes both curated and calculated orthologs and homologs for genes represented in
UniGene and LocusLink for human, mouse, rat, and
zebrafish.
WWW Virtual Library Model Organisms
http://ceolas.org/VL/mo/
mouse
Mus musculus, mice:
Mouse Genetics, Lee Silver, Oxford Univ. Press, 1995, adapted for
the web http://www.informatics.jax.org/silver/
Mouse Genome Informatics, Jackson
Laboratory, US http://www.informatics.jax.org/
Mouse Genome Informatics Glossary, Jackson
Laboratory,
US http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=glossaryIndex&print=no
Mouse Phenome Database
, Jackson Laboratory, US http://phenome.jax.org/
NHGRI, Background on the mouse as a model organism
https://www.genome.gov/10005834/background-on-mouse-as-a-model-organism/
Narrower terms: knockout mice, transgenic mice
Muridae:
A family of the order Rodentia containing 250
genera including the two genera Mus and Rattus, from which the
laboratory inbred strains are developed. The fifteen subfamilies are HESPEROMYINAE
(New World mice and rats), Cricetinae, Spalacinae, Myospalacinae,
Lophiomyinae, Platacanthomyinae, Nesomyinae, Otomyinae, Rhizomyinae, MICROTINAE
(Arvicolinae), GERBILLINAE, Dendromurinae, Cricetomyinae, Murinae (Old World
mice and rats), and Hydromyinae. MeSH, 1982
murine: Of, pertaining to, or
characteristic of, the mouse,
rat or (more generally) any mammal of the family Muridae.
https://en.wiktionary.org/wiki/murine
Pichia:
Yeast-like ascomycetous fungi of the family Saccharomycetaceae,
order SACCHAROMYCETALES isolated from exuded tree sap. MeSH, 1991
rat, Rattus Norvegicus: Used
extensively as a model organism for studying normal and disease processes
in the human, primarily because of an extensive body of knowledge of rat
physiological mechanisms, a significant number of rat models that mimic
human diseases, the ease of breeding the rat, and the ability to generate
inbred congenic and consomic rat strains. Once genes are identified in
rats, pathophysiological mechanisms can be elucidated lending clues to
the identification of human genetic counter- parts. [Rat Genome Database
Request For Applications, NIH April 1999] http://grants.nih.gov/grants/guide/rfa-files/RFA-HL-99-013.html
The common name for the species Rattus norvegicus. MeSH MeSH also has
a number of additional terms for inbred rats.
Rat Genome Resources, NCBI, US
http://www.ncbi.nlm.nih.gov/genome/guide/rat/index.html
Rat Genome Data, Medical College of Wisconsin , US http://rgd.mcw.edu/
Rat Genome glossary
, Medical
College of Wisconsin, US
https://rgd.mcw.edu/wg/help3/glossary/
Narrower term: knockout rats
Saccharomyces cerevisae (S.
cerevisae):
A species of the genus SACCHAROMYCES, family Saccharomycetaceae,
order Saccharomycetales, known as "baker's" or
"brewer's" yeast. The dried form is used as a dietary supplement.
MeSH, 1973
Yeast, perhaps the best understood eukaryotic organism
at the molecular and cellular levels. However [forward genetics] had, prior
to the systematic sequencing of the yeast genome (completed in 1996) resulted
in the discovery of less than half of yeast genes. Now the yeast genomics
community has turned to a large- scale, high- throughput approach to determining
gene function, largely based on reverse genetics. Since yeast is the first
eukaryotic model organism whose genome has been completely sequenced, many
of the issues currently being faced by the yeast genomics community will
eventually be of concern to people working with other organisms, including
humans.
Yeast can in certain cases serve as a model of human
disease ... The general rationale for this strategy is that many core cellular
processes (as opposed to processes involved in differentiation and development,
integration of tissues and organ systems, and activities of specialized cells
and tissues) are conserved between yeast and mammals. In fact, many molecules
and pathways that are known to be involved in processes that go awry in cancer
(e.g., the cell cycle and its control, DNA repair, telomere maintenance)
were either first discovered by yeast researchers, or research in yeast made
major contributions to their understanding.
Saccharomyces
Genome Deletion
Project
http://sequence-www.stanford.edu/group/yeast_deletion_project/deletions3.html
slime mold: See Dictyostelium discoideum
transgenic: An experimentally produced organism in which DNA
has been artificially introduced and incorporated into the organism’s germ
line, usually by injecting the foreign DNA into the nucleus of a fertilized
embryo. [NHGRI]
Plants can be transgenic as well as animal, though the field is not
as highly developed. Transgenics can be a means of production as
well as a way of systematic experimenting with knockouts.
Related terms:
knockout mice; knockdown,
knockin, knockout
transgenic mice:
Laboratory mice that have been produced from a
genetically manipulated egg or embryo. MeSH, 1988
virtual organism: http://openworm.org/
worm: See Caenorhabditis elegans (C.
elegans)
WormBase nomenclature
https://wormbase.org/about/userguide/nomenclature#efl64d8i17hkg209c53majb--10
as c elegans Xenopus
frog:
An aquatic
genus of the family, Pipidae, occurring in Africa and
distinguished by having black horny claws on three inner hind toes. MeSH, 1972
Xenopus Gene Collections, NIH
https://genecollections.nci.nih.gov/XGC/
Xenbase
A Xenopus Resource http://www.xenbase.org/
Xenopus laevis:
The commonest and widest ranging species of the
clawed "frog" (Xenopus) in Africa. This species is used extensively in
research. There is now a significant population in California derived from
escaped laboratory animals. MeSH, 1981
yeast:
Perhaps the best- studied eukaryotic organism. Its experimental tractability, combined with the remarkable conservation of gene function throughout evolution, makes yeast the ideal model genetic organism. Yeast is a
non- pathogenic model of fungal pathogens used to identify antifungal targets suitable for drug development and to elucidate mechanisms of action of antifungal agents. As a model of fundamental cellular processes and metabolic pathways of the human, yeast has improved our understanding and facilitated the molecular analysis of many disease genes. The completion of the
Saccharomyces genome sequence helped launch the
post- genomic era, focusing on functional analyses of whole genomes. Yeast paved the way for the systematic analysis of large and complex genomes by serving as a test bed for novel experimental approaches and technologies, tools that are fast becoming the standard
in drug discovery research. D. Ma, Applications of yeast in drug
discovery, Progress Drug Research 57: 117- 162, 2001
If not otherwise specified generally refers to Saccharomyces cerevisae. Other species of yeast,
including Schizosaccharomyces pombe are also studied. Narrower terms: pichia, Saccharomyces cerevisae
zebrafish Danio rerio:
A
species of North American fishes of the family Cyprinidae. They
are used in embryological studies and to study the effects of certain chemicals
on development. MeSH, 1991
Transparent embryos facilitate functional genomics
research.
Model organisms resources
Mouse Genome Informatics Glossary, Jackson Lab, US,
http://www.informatics.jax.org/javawi2/servlet/WIFetch?page=glossaryIndex&printFormat=footer
RGD Glossary, Rat Genome Database Glossary Medical College of Wisconsin
https://rgd.mcw.edu/wg/help3/glossary/
Zebrafish Ontology Search
Zebrafish Information Network,
https://zfin.org/action/ontology/search
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